The medico-legal organisation said this suggested that a rise in complaints in 2009/10 was caused by changes to the NHS complaints system, rather than declining standards.
The finding comes as the GMC reported that slipping medical standards were not to blame for a 30% increase in fitness-to-practise referrals since 2004.
The MDU research found complaints were up 10% in 2009/10 but then fell by 11% in 2010/11.
It also found that although complaints increased in 2009/10, the proportion referred on to the health service ombudsman dropped by a third.
The MDU said the most common reasons for complaints were allegations of delayed or wrong diagnosis, problems with communication or issues with prescribing.
MDU medico-legal adviser Dr Jacqueline Phillips, who carried out the research, said the new NHS complaints system introduced in 2009 was likely to be behind the increase in complaints in 2009/10.
She said: 'Looking at the trends it is clear that the new complaints procedure was a factor. This meant practices were notifying us more about complaints and looking for advice on how to handle matters. The rise did not reflect a decline in medical standards.'
Meanwhile, a GMC investigation showed the increase in fitness-to-practise referrals over recent years was due to improved systems of oversight and monitoring by employers.
GMC chief executive Niall Dickson said: 'More complaints about doctors do not necessarily mean standards are slipping.
It could be a sign that the systems to identify problems are improving.
'In addition, rather than keeping quiet about problems, doctors are more likely to speak up when they see anything that could pose a risk to patient safety. And that is exactly as it should be.'